5,6-Dioxo-1,10-phenanthrolin-1-ium nitrate

Abbasi, A.; Badiei, A.; Tarighi, S.

doi:10.1107/S1600536807066172

organic compounds

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ISSN: 2056-9890

Volume 64| Part 1| January 2008| Page o290

https://doi.org/10.1107/S1600536807066172

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5,6-Dioxo-1,10-phenanthrolin-1-ium nitrate

Alireza Abbasi,^a ^* Alireza Badiei ^a and Sara Tarighi ^a

^aSchool of Chemistry, University College of Science, University of Tehran, Tehran, Iran
^*Correspondence e-mail: aabbasi@khayam.ut.ac.ir

(Received 29 November 2007; accepted 8 December 2007; online 18 December 2007)

In the title salt, C₁₂H₇N₂O₂⁺·NO₃⁻, the monoprotonated cation is connected to the nitrate anion by a hydrogen bond. Weak C—H⋯O hydrogen bonds hold the planar cations together in a layer structure.

Related literature

For related literature, see Fujihara et al. (2004 ); Larsson & Ohström (2004 ). For the bromide salt, see: Bomfim et al. (2003 ).

Experimental

Crystal data

C₁₂H₇N₂O₂⁺·NO₃⁻
M_r = 273.21
Monoclinic, C 2/c
a = 14.4860 (19) Å
b = 12.5177 (13) Å
c = 13.4535 (16) Å
β = 101.720 (12)°
V = 2388.7 (5) Å³
Z = 8
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 290 (2) K
0.30 × 0.10 × 0.08 mm

Data collection

Oxford Diffraction Xcalibur 3 CCD diffractometer
Absorption correction: numerical (X-RED; Stoe & Cie, 1997 ) T_min = 0.960, T_max = 0.989
7311 measured reflections
2095 independent reflections
635 reflections with I > 2σ(I)
R_int = 0.068

Refinement

R[F² > 2σ(F²)] = 0.038
wR(F²) = 0.060
S = 0.83
2095 reflections
182 parameters
H-atom parameters constrained
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.14 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O5	0.86	1.95	2.703 (4)	145
C8—H8⋯O5ⁱ	0.93	2.48	3.396 (4)	167
C9—H9⋯O4ⁱ	0.93	2.71	3.359 (5)	128
C4—H4⋯O4ⁱⁱ	0.93	2.61	3.323 (4)	134
C3—H3⋯O3ⁱⁱ	0.93	2.40	3.209 (4)	146
C10—H10⋯O1ⁱⁱⁱ	0.93	2.47	3.318 (5)	151
C5—H5⋯O2^iv	0.93	2.37	3.266 (5)	162
Symmetry codes: (i) $[x+{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ ; (ii) $[x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ ; (iii) $[x-{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ ; (iv) $[x-{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ .

Data collection: CrysAlis CCD (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Versions 1.171.29.2. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Versions 1.171.29.2. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 2001 ); software used to prepare material for publication: PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536807066172/ng2405sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807066172/ng2405Isup2.hkl

checkCIF report

Comment top

From a survey of the Cambridge Structural Database [version 5.28, updated Jan. 2007], we found two complexes containing O-protonated pdon (Fujihara, et al., 2004; Larsson, & Ohström, 2004). However, up to now, only one molecule is reported for the N-protonated pdon (C₁₂H₇N₂O₂⁺, Hpdon) with bromide ions as counter ion (Bomfim et al., 2003).

The molecular structure and atom-labeling scheme for (I) are shown in Fig. 1. There is a relatively strong hydrogen bond between the nitrate ion and to the protonated nitrogen atom in Hpdon (N1—H1···O5, 2.703 (4) Å). Weak C–H···O hydrogen bonds hold the approximately planar cations together in a layer structure (Fig. 2). The packing of the layers is similar to that in the bromide salt of Hpdon (Bomfim et al., 2003) without specific directional interactions between the layers. Ring A (C1–C5/N1), B (C6–C10/N2) and C (C1/C2/C12/C11/C7/C6) in the cation (C₁₂H₇N₂O₂⁺, Hpdon) is approximately planar. The interplanar angle between the least-square planes defined by ring A and two other rings, B and C, are 1.69 (5)° and 1.17 (5)°, respectively. While, rings B and C are almost planar, 0.52 (5)°. However, the C—N—C angle is affected by protonation and causes to increase from 116.6 (3)° to 122.7 (3)° in the rings B and A, respectively. Similar effect has also been shown in the previously reported Hpdon bromide by increasing from 116.8 (3)° to 123.2 (3)° for the corresponding values. The comparison of the torsion angle, O1—C12—C11—O2, 2.5 (6)°, in (I) with the molecular pdon indicates that the N-protonation in (I) doesn't significantly affect on dione groups.

Related literature top

For related literature, see Fujihara et al. (2004); Larsson & Ohström (2004). For the bromide salt, see: Bomfim et al. (2003).

Experimental top

The title compound was obtained during the reaction of thorium nitrate, Th(NO₃)₄.5H₂O (Merck, 99%), and 1,10-phenanthroline-5,6-dione (Aldrich, 97%) in ethanolic solution. Pale-yellow crystals of Hpdon were taken from the obtained greenish precipitates. The presence of water in the ethanolic solution and the high basicity of dione ligand can be the reason for the protonation, providing the C₁₂H₇N₂O₂⁺, Hpdon cation. Thin fragile layer crystals were obtained by recrystallization from acetonitrile.

Structure description top

For related literature, see Fujihara et al. (2004); Larsson & Ohström (2004). For the bromide salt, see: Bomfim et al. (2003).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2003); cell refinement: CrysAlis CCD (Oxford Diffraction, 2003); data reduction: CrysAlis RED (Oxford Diffraction, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: PLATON (Spek, 2003).

Figures top

	Fig. 1. Molecular structure of (I), with 50% probability displacement ellipsoids. H atoms are shown as circles of arbitrary radii.
	Fig. 2. Packing view for (I), showing the hydrogen bonds as dashed lines.

5,6-Dioxo-1,10-phenanthrolin-1-ium nitrate top

Crystal data top

C₁₂H₇N₂O₂⁺·NO₃⁻	F(000) = 1120
M_r = 273.21	D_x = 1.519 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 7311 reflections
a = 14.4860 (19) Å	θ = 3.5–25.0°
b = 12.5177 (13) Å	µ = 0.12 mm⁻¹
c = 13.4535 (16) Å	T = 290 K
β = 101.720 (12)°	Needle, pale-yellow
V = 2388.7 (5) Å³	0.30 × 0.10 × 0.08 mm
Z = 8

Data collection top

Oxford Diffraction Xcalibur 3 CCD diffractometer	2095 independent reflections
Radiation source: fine-focus sealed tube	635 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.068
Detector resolution: 12 pixels mm^-1	θ_max = 25.0°, θ_min = 3.8°
ω–scans at different φ	h = −17→17
Absorption correction: numerical (X-RED; Stoe & Cie, 1997)	k = −14→14
T_min = 0.960, T_max = 0.989	l = −10→15
7311 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.038	H-atom parameters constrained
wR(F²) = 0.060	w = 1/[σ²(F_o²) + (0.01P)²] where P = (F_o² + 2F_c²)/3
S = 0.83	(Δ/σ)_max < 0.001
2095 reflections	Δρ_max = 0.31 e Å⁻³
182 parameters	Δρ_min = −0.14 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.00072 (4)

Crystal data top

C₁₂H₇N₂O₂⁺·NO₃⁻	V = 2388.7 (5) Å³
M_r = 273.21	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 14.4860 (19) Å	µ = 0.12 mm⁻¹
b = 12.5177 (13) Å	T = 290 K
c = 13.4535 (16) Å	0.30 × 0.10 × 0.08 mm
β = 101.720 (12)°

Data collection top

Oxford Diffraction Xcalibur 3 CCD diffractometer	2095 independent reflections
Absorption correction: numerical (X-RED; Stoe & Cie, 1997)	635 reflections with I > 2σ(I)
T_min = 0.960, T_max = 0.989	R_int = 0.068
7311 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.060	H-atom parameters constrained
S = 0.83	Δρ_max = 0.31 e Å⁻³
2095 reflections	Δρ_min = −0.14 e Å⁻³
182 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.85417 (17)	−0.13522 (19)	0.12439 (18)	0.0673 (8)
O2	0.85003 (19)	0.08376 (19)	0.1238 (2)	0.0834 (10)
O3	0.30299 (14)	0.0377 (2)	0.07097 (16)	0.0649 (7)
O4	0.22236 (15)	−0.03456 (19)	0.17219 (15)	0.0613 (6)
O5	0.34903 (16)	−0.11186 (18)	0.14632 (16)	0.0622 (7)
N1	0.52797 (19)	−0.1426 (2)	0.12265 (18)	0.0439 (9)
H1	0.4776	−0.1063	0.1230	0.053*
N2	0.5205 (2)	0.0692 (2)	0.1274 (2)	0.0488 (9)
N3	0.29121 (19)	−0.0361 (3)	0.1292 (2)	0.0476 (8)
C1	0.6089 (3)	−0.0896 (3)	0.1224 (2)	0.0370 (9)
C2	0.6903 (3)	−0.1473 (3)	0.1211 (2)	0.0374 (10)
C3	0.6870 (3)	−0.2573 (3)	0.1201 (2)	0.0528 (11)
H3	0.7411	−0.2969	0.1191	0.063*
C4	0.6018 (3)	−0.3086 (3)	0.1207 (2)	0.0550 (11)
H4	0.5986	−0.3828	0.1198	0.066*
C5	0.5228 (3)	−0.2490 (3)	0.1224 (2)	0.0502 (11)
H5	0.4657	−0.2826	0.1235	0.060*
C6	0.6062 (3)	0.0275 (3)	0.1258 (2)	0.0380 (9)
C7	0.6867 (3)	0.0879 (3)	0.1278 (2)	0.0421 (10)
C8	0.6798 (3)	0.1978 (3)	0.1312 (2)	0.0534 (13)
H8	0.7320	0.2411	0.1319	0.064*
C9	0.5922 (3)	0.2415 (3)	0.1336 (2)	0.0589 (12)
H9	0.5852	0.3151	0.1369	0.071*
C10	0.5151 (3)	0.1749 (3)	0.1308 (3)	0.0589 (13)
H10	0.4568	0.2058	0.1314	0.071*
C11	0.7780 (3)	0.0351 (4)	0.1244 (2)	0.0526 (10)
C12	0.7807 (3)	−0.0894 (3)	0.1227 (2)	0.0469 (11)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0405 (19)	0.064 (2)	0.102 (2)	0.0165 (15)	0.0270 (16)	0.0046 (15)
O2	0.051 (2)	0.062 (2)	0.146 (2)	−0.0150 (16)	0.0412 (18)	−0.0002 (17)
O3	0.0736 (19)	0.0573 (18)	0.0696 (16)	0.0079 (15)	0.0282 (13)	0.0205 (15)
O4	0.0508 (18)	0.0664 (15)	0.0730 (16)	0.0081 (16)	0.0276 (13)	0.0048 (14)
O5	0.0453 (17)	0.0477 (18)	0.0977 (18)	0.0163 (14)	0.0242 (14)	0.0116 (15)
N1	0.036 (2)	0.038 (2)	0.0605 (19)	0.0038 (18)	0.0143 (17)	0.0013 (19)
N2	0.054 (2)	0.035 (2)	0.0620 (19)	0.0086 (17)	0.0214 (18)	−0.0027 (17)
N3	0.041 (2)	0.051 (2)	0.053 (2)	−0.005 (2)	0.0144 (17)	−0.001 (2)
C1	0.034 (3)	0.038 (3)	0.041 (2)	−0.007 (2)	0.012 (2)	−0.003 (2)
C2	0.037 (3)	0.033 (3)	0.044 (2)	0.008 (2)	0.011 (2)	0.006 (2)
C3	0.056 (3)	0.043 (3)	0.065 (3)	0.009 (3)	0.023 (2)	0.002 (2)
C4	0.067 (4)	0.034 (3)	0.066 (3)	0.001 (3)	0.020 (2)	0.004 (2)
C5	0.050 (3)	0.035 (3)	0.068 (3)	−0.007 (2)	0.017 (2)	0.000 (2)
C6	0.037 (3)	0.035 (3)	0.042 (2)	−0.001 (3)	0.0093 (19)	−0.010 (3)
C7	0.038 (3)	0.036 (3)	0.053 (2)	0.002 (2)	0.011 (2)	0.002 (2)
C8	0.060 (4)	0.030 (3)	0.070 (3)	−0.005 (2)	0.012 (2)	0.003 (2)
C9	0.073 (4)	0.037 (3)	0.065 (3)	0.015 (3)	0.010 (3)	−0.001 (2)
C10	0.058 (4)	0.045 (3)	0.075 (3)	0.005 (2)	0.016 (3)	−0.003 (2)
C11	0.052 (3)	0.051 (3)	0.059 (2)	−0.002 (3)	0.021 (2)	0.001 (3)
C12	0.050 (3)	0.048 (3)	0.046 (2)	0.000 (3)	0.018 (2)	−0.002 (2)

Geometric parameters (Å, º) top

O1—C12	1.206 (4)	C3—C4	1.392 (4)
O2—C11	1.210 (3)	C3—H3	0.9300
O3—N3	1.244 (3)	C4—C5	1.371 (4)
O4—N3	1.251 (3)	C4—H4	0.9300
O5—N3	1.256 (3)	C5—H5	0.9300
N1—C5	1.335 (4)	C6—C7	1.385 (4)
N1—C1	1.347 (4)	C7—C8	1.381 (4)
N1—H1	0.8600	C7—C11	1.488 (4)
N2—C10	1.326 (4)	C8—C9	1.387 (4)
N2—C6	1.350 (4)	C8—H8	0.9300
C1—C2	1.387 (4)	C9—C10	1.389 (4)
C1—C6	1.467 (4)	C9—H9	0.9300
C2—C3	1.377 (4)	C10—H10	0.9300
C2—C12	1.492 (4)	C11—C12	1.559 (4)

C5—N1—C1	122.7 (3)	N2—C6—C7	124.1 (4)
C5—N1—H1	118.7	N2—C6—C1	114.7 (4)
C1—N1—H1	118.7	C7—C6—C1	121.2 (4)
C10—N2—C6	116.6 (3)	C8—C7—C6	118.5 (4)
O3—N3—O4	120.3 (3)	C8—C7—C11	120.9 (4)
O3—N3—O5	120.3 (3)	C6—C7—C11	120.5 (4)
O4—N3—O5	119.4 (3)	C7—C8—C9	117.8 (4)
N1—C1—C2	119.1 (4)	C7—C8—H8	121.1
N1—C1—C6	117.6 (4)	C9—C8—H8	121.1
C2—C1—C6	123.3 (4)	C8—C9—C10	119.8 (4)
C3—C2—C1	119.5 (4)	C8—C9—H9	120.1
C3—C2—C12	121.0 (4)	C10—C9—H9	120.1
C1—C2—C12	119.5 (4)	N2—C10—C9	123.1 (4)
C2—C3—C4	119.4 (4)	N2—C10—H10	118.4
C2—C3—H3	120.3	C9—C10—H10	118.4
C4—C3—H3	120.3	O2—C11—C7	123.4 (5)
C5—C4—C3	119.6 (4)	O2—C11—C12	118.6 (4)
C5—C4—H4	120.2	C7—C11—C12	118.0 (4)
C3—C4—H4	120.2	O1—C12—C2	122.5 (4)
N1—C5—C4	119.8 (4)	O1—C12—C11	120.0 (4)
N1—C5—H5	120.1	C2—C12—C11	117.5 (4)
C4—C5—H5	120.1

C5—N1—C1—C2	0.5 (5)	N2—C6—C7—C11	−179.1 (3)
C5—N1—C1—C6	−178.2 (3)	C1—C6—C7—C11	1.2 (5)
N1—C1—C2—C3	0.0 (5)	C6—C7—C8—C9	0.7 (5)
C6—C1—C2—C3	178.6 (3)	C11—C7—C8—C9	179.5 (3)
N1—C1—C2—C12	−178.9 (3)	C7—C8—C9—C10	−1.0 (5)
C6—C1—C2—C12	−0.3 (5)	C6—N2—C10—C9	−0.5 (5)
C1—C2—C3—C4	−0.1 (5)	C8—C9—C10—N2	1.0 (6)
C12—C2—C3—C4	178.7 (3)	C8—C7—C11—O2	−0.4 (5)
C2—C3—C4—C5	−0.2 (5)	C6—C7—C11—O2	178.4 (3)
C1—N1—C5—C4	−0.8 (5)	C8—C7—C11—C12	178.9 (3)
C3—C4—C5—N1	0.6 (6)	C6—C7—C11—C12	−2.3 (5)
C10—N2—C6—C7	0.2 (5)	C3—C2—C12—O1	−0.9 (5)
C10—N2—C6—C1	179.8 (3)	C1—C2—C12—O1	178.0 (4)
N1—C1—C6—N2	−0.9 (5)	C3—C2—C12—C11	−179.6 (3)
C2—C1—C6—N2	−179.5 (3)	C1—C2—C12—C11	−0.8 (4)
N1—C1—C6—C7	178.7 (3)	O2—C11—C12—O1	2.5 (6)
C2—C1—C6—C7	0.1 (5)	C7—C11—C12—O1	−176.8 (3)
N2—C6—C7—C8	−0.3 (5)	O2—C11—C12—C2	−178.6 (3)
C1—C6—C7—C8	−179.9 (3)	C7—C11—C12—C2	2.1 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O5	0.86	1.95	2.703 (4)	145
C8—H8···O5ⁱ	0.93	2.48	3.396 (4)	167
C9—H9···O4ⁱ	0.93	2.71	3.359 (5)	128
C4—H4···O4ⁱⁱ	0.93	2.61	3.323 (4)	134
C3—H3···O3ⁱⁱ	0.93	2.40	3.209 (4)	146
C10—H10···O1ⁱⁱⁱ	0.93	2.47	3.318 (5)	151
C5—H5···O2^iv	0.93	2.37	3.266 (5)	162

Symmetry codes: (i) x+1/2, y+1/2, z; (ii) x+1/2, y−1/2, z; (iii) x−1/2, y+1/2, z; (iv) x−1/2, y−1/2, z.

Experimental details

Crystal data
Chemical formula	C₁₂H₇N₂O₂⁺·NO₃⁻
M_r	273.21
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	290
a, b, c (Å)	14.4860 (19), 12.5177 (13), 13.4535 (16)
β (°)	101.720 (12)
V (Å³)	2388.7 (5)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.30 × 0.10 × 0.08

Data collection
Diffractometer	Oxford Diffraction Xcalibur 3 CCD
Absorption correction	Numerical (X-RED; Stoe & Cie, 1997)
T_min, T_max	0.960, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections	7311, 2095, 635
R_int	0.068
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.060, 0.83
No. of reflections	2095
No. of parameters	182
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.31, −0.14

Computer programs: CrysAlis CCD (Oxford Diffraction, 2003), CrysAlis RED (Oxford Diffraction, 2003), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), DIAMOND (Brandenburg, 2001), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O5	0.86	1.95	2.703 (4)	145.1
C8—H8···O5ⁱ	0.93	2.48	3.396 (4)	167.0
C9—H9···O4ⁱ	0.93	2.71	3.359 (5)	127.9
C4—H4···O4ⁱⁱ	0.93	2.61	3.323 (4)	133.9
C3—H3···O3ⁱⁱ	0.93	2.40	3.209 (4)	145.8
C10—H10···O1ⁱⁱⁱ	0.93	2.47	3.318 (5)	150.9
C5—H5···O2^iv	0.93	2.37	3.266 (5)	162.0

Symmetry codes: (i) x+1/2, y+1/2, z; (ii) x+1/2, y−1/2, z; (iii) x−1/2, y+1/2, z; (iv) x−1/2, y−1/2, z.

Acknowledgements

This work was supported by grants from the University of Tehran and the Swedish Research Council. The authors are grateful to Professor Magnus Sandström for his support.

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